We detected and characterized two distinct scuticociliate ciliates inside Acropora corals in the South China Sea. One, voraciously foraging on Symbiodinium, resembled the brown band disease of ciliates. The other, which is closely related to Paranophrys magna, grazed on detritus instead of Symbiodinium. These two ciliates may serve contrasting functions (competitor versus "cleaner") in the coral-ciliate-Symbiodinium triangular relationship.Various ciliates have been found to dwell in coral reefs (1,2,5,6,9,15,16,18,23,24), but their genetic and physiological diversities remain poorly understood. Best studied were those associated with coral diseases, such as skeletoneroding band (SEB) (1, 17) and brown band syndrome (BrB) (5, 24). BrB causes a brown zone on the coral, often sandwiched by healthy tissue and exposed white skeleton (24), which occurs when a large mass of a scuticociliate ciliate is present. BrB has been described for three coral families (Acroporidae, Pocilloporidae, and Faviidae) on the Great Barrier Reef, Australia (5, 21, 24), and for Porites astreoides and Montastraea faveolata in Florida (8). The responsible ciliate has been classified in different lineages (4,8), but a recent molecular analysis based on the 18S rRNA gene (18S rDNA) identified it as a novel species closely related to the scuticociliate genera Uronema and Paranophrys (6). This ciliate was observed to consume the spat of the host coral (8) and to intensively ingest the coral's essential endosymbiont Symbiodinium; the ingested alga could remain intact and photosynthetically active within the ciliate after ingestion (21). Whether other ciliates cohabit with BrB ciliates in the coral and whether they would play different ecological functions in the coral microcosm are of high interest but remain obscure. In an attempt to address these issues, we found two closely related but distinct ciliates from two Acropora corals in the South China Sea. By culturing, microscopic examination, molecular (18S rDNA) analysis of a community DNA extract, and microscopic examination of isolated single cells and cultures, we observed distinct morphologies, phylogenetic positions, and trophic behaviors in these two ciliates.Sampling of corals and intracavity microbial assemblages. Coral branches were collected at 18°12ЈN, 109°28ЈE (latitude, longitude) at a depth of 1.6 m at Sanya, off Hainan Island in the South China Sea. The temperature was 27.1°C. After collection, each coral branch was transported in ambient seawater and transported to the laboratory in Sanya within 45 min. After the surface was rinsed with 0.45-m-filtered seawater, the internal content of the coral (endosymbionts) was washed off using a Waterpik Ultra dental water jet (WP70EC; Alibaba, Shenzhen, China). Six 2-ml subsamples were preserved in 1% formaldehyde and immediately frozen in liquid nitrogen. The remainder was kept at ambient temperature for culturing. The corals were identified as Acropora microclados and Acropora hyacinthus as previously described (22). In situ and laborato...